Iron oxide copper-gold (IOCG) deposits form in spatial and genetic relation to hydrothermal iron oxide-alkali-calcic-hydrolytic alteration and thus show a mappable zonation of mineral assemblages toward the orebody. The mineral zonation of a breccia matrix-hosted orebody is efficiently mapped by regularly spaced samples analyzed by the scanning electron microscopy-integrated mineral analyzer technique. The method results in quantitative estimates of the mineralogy and allows the reliable recognition of characteristic alteration as well as mineralization-related mineral assemblages from detailed mineral maps. The Ernest Henry deposit is located in the Cloncurry district of Queensland and is one of Australia’s significant IOCG deposits. It is known for its association of K-feldspar altered clasts with iron oxides and chalcopyrite in the breccia matrix. Our mineral mapping approach shows that the hydrothermal alteration resulted in a characteristic zonation of minerals radiating outward from the pipe-shaped orebody. The mineral zonation is the result of a sequence of sodic alteration followed by potassic alteration, brecciation, and, finally, by hydrolytic (acid) alteration. The hydrolytic alteration primarily affected the breccia matrix and was related to economic mineralization. Alteration halos of individual minerals such as pyrite and apatite extend dozens to hundreds of meters beyond the limits of the orebody into the host rocks. Likewise, the Fe-Mg ratio in hydrothermal chlorites changes systematically with respect to their distance from the orebody. Geochemical data obtained from portable X-ray fluorescence (p-XRF) and petrophysical data acquired from a magnetic susceptibility meter and a gamma-ray spectrometer support the mineralogical data and help to accurately identify mineral halos in rocks surrounding the ore zone. Specifically, the combination of mineralogical data with multielement data such as P, Mn, As, P, and U obtained from p-XRF and positive U anomalies from radiometric measurements has potential to direct an exploration program toward higher Cu-Au grades.